2-48422566-T-C

Variant names:

• chr2-48422566-T-C
• rs7565792

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.575 in 152,080 control chromosomes in the GnomAD database, including 25,455 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (25455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87361 AN: 151962 Hom.: 25442 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.577

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.575 AC: 87425 AN: 152080 Hom.: 25455 Cov.: 32 AF XY: 0.570 AC XY: 42341 AN XY: 74342

African (AFR) AF: 0.549 AC: 22771 AN: 41460

American (AMR) AF: 0.475 AC: 7258 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1966 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2741 AN: 5180

South Asian (SAS) AF: 0.470 AC: 2268 AN: 4824

European-Finnish (FIN) AF: 0.582 AC: 6150 AN: 10568

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42306 AN: 67998

Other (OTH) AF: 0.575 AC: 1214 AN: 2112

Alfa AF: 0.603 Hom.: 77457

Bravo AF: 0.567

Asia WGS AF: 0.490 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.092
DANN	Benign	0.17
PhyloP100		-3.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7565792; hg19: chr2-48649705;